nf-illumina2lineage

A reproducible and modular Nextflow pipeline for SARS-CoV-2 genome assembly and lineage analysis from Illumina paired-end sequencing data.

Overview

This pipeline automates:

• Read quality control
• Reference-based mapping
• Primer clipping
• Variant calling
• Consensus generation
• Lineage assignment
• Phylogenetic analysis

It is based on best-practice tools and developed as part of the SARS-2 Bioinformatics & Data Science course by Freie Universität Berlin and the Robert Koch Institute.

Quickstart

git clone https://github.com/bibymaths/nf-illumina2lineage.git
cd nf-illumina2lineage

💡 See docs/quickstart.md for full details.

Inputs

• Illumina paired-end .fastq.gz files
• SARS-CoV-2 reference genome (downloaded automatically)

Outputs

• QC reports: FastQC, Fastp, MultiQC
• BAM & VCF files
• Consensus FASTA sequences
• Pangolin lineage annotations
• Phylogenetic tree (.treefile)

For a full output structure, see docs/outputs.md.

Dependencies

Managed via mamba or Docker:

• QC: fastqc, fastp, multiqc
• Mapping: minimap2, samtools, bamclipper
• Variant Calling: freebayes, vcftools, bcftools
• Consensus: vcfR, bcftools, president
• Lineage & MSA: pangolin, mafft, iqtree

Documentation

Complete documentation is available under the docs/ folder and rendered via MkDocs. Includes:

• Pipeline overview
• Process details
• Parameters
• Container usage
• Lineage QC

License

This project is licensed under the BSD 3-Clause License. See LICENSE.

Author

Abhinav Mishra
Email: [email protected]

Acknowledgments

Developed during the SARS-2 Bioinformatics & Data Science course at FU Berlin & RKI, under guidance of Max von Kleist and Martin Hölzer.

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